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- PDB-8r1m: Structure of TxGH116 with covalently bound N-azido-octyl aziridine -

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Basic information

Entry
Database: PDB / ID: 8r1m
TitleStructure of TxGH116 with covalently bound N-azido-octyl aziridine
ComponentsGlucosylceramidase
KeywordsHYDROLASE / Beta-glucosidase / covalent complex / aziridine
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / : / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOffen, W.A. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: Chem Sci / Year: 2024
Title: Selective labelling of GBA2 in cells with fluorescent beta-d-arabinofuranosyl cyclitol aziridines.
Authors: Su, Q. / Louwerse, M. / Lammers, R.F. / Maurits, E. / Janssen, M. / Boot, R.G. / Borlandelli, V. / Offen, W.A. / Linzel, D. / Schroder, S.P. / Davies, G.J. / Overkleeft, H.S. / Artola, M. / Aerts, J.M.F.G.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,66812
Polymers183,5882
Non-polymers1,08010
Water15,853880
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4007
Polymers91,7941
Non-polymers6066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2685
Polymers91,7941
Non-polymers4744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.975, 165.149, 178.921
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 31 - 802 / Label seq-ID: 16 - 787

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucosylceramidase


Mass: 91794.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Gene: Thexy_2211 / Production host: Escherichia coli (E. coli) / References: UniProt: F6BL85

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Non-polymers , 5 types, 890 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-XHR / (1R,2R,3R,4S)-4-[8-(azanyldiazenyl)octylamino]-3-(hydroxymethyl)cyclopentane-1,2-diol


Mass: 302.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30N4O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3000, ammonium sulfate, MES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.9→56.16 Å / Num. obs: 129333 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.996 / Rpim(I) all: 0.079 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6302 / CC1/2: 0.554 / Rpim(I) all: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→56.095 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.154 / Average fsc free: 0.958 / Average fsc work: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 6300 4.881 %RANDOM
Rwork0.1771 122777 --
all0.179 ---
obs-129077 99.863 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.706 Å2-0 Å20 Å2
2--0.26 Å2-0 Å2
3----1.966 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12403 0 53 880 13336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213027
X-RAY DIFFRACTIONr_bond_other_d00.01611748
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.80817717
X-RAY DIFFRACTIONr_angle_other_deg0.5931.76927168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12951600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.114526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.443102161
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.43410628
X-RAY DIFFRACTIONr_chiral_restr0.0770.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215509
X-RAY DIFFRACTIONr_gen_planes_other0.0140.023107
X-RAY DIFFRACTIONr_nbd_refined0.2140.22747
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.210873
X-RAY DIFFRACTIONr_nbtor_refined0.190.26361
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.26110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2883
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2410.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.27
X-RAY DIFFRACTIONr_nbd_other0.1530.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.217
X-RAY DIFFRACTIONr_mcbond_it1.8672.396271
X-RAY DIFFRACTIONr_mcbond_other1.8672.396271
X-RAY DIFFRACTIONr_mcangle_it2.7994.2937866
X-RAY DIFFRACTIONr_mcangle_other2.7994.2947867
X-RAY DIFFRACTIONr_scbond_it2.0922.5246756
X-RAY DIFFRACTIONr_scbond_other2.0922.5246757
X-RAY DIFFRACTIONr_scangle_it3.254.5619835
X-RAY DIFFRACTIONr_scangle_other3.2494.5619836
X-RAY DIFFRACTIONr_lrange_it4.57523.15915605
X-RAY DIFFRACTIONr_lrange_other4.57523.15915606
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0527457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.099950.05009
12AX-RAY DIFFRACTIONLocal ncs0.099950.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.3394820.31689020.31794140.9240.92999.68130.309
1.949-2.0030.2874520.26587120.26691840.9320.94799.78220.256
2.003-2.0610.2874650.24485010.24689800.9430.95699.84410.231
2.061-2.1240.2664190.2282950.22287260.950.96599.86250.205
2.124-2.1940.2444030.20880180.2184270.9560.9799.92880.191
2.194-2.270.2764150.22177100.22481370.9510.9799.85250.201
2.27-2.3560.273900.19274940.19678990.9560.97799.81010.168
2.356-2.4520.2353660.1872540.18376330.9660.9899.82970.156
2.452-2.5610.2633410.17469520.17872990.9640.98199.91780.15
2.561-2.6850.2343450.16466290.16769840.9690.98499.85680.142
2.685-2.830.2423290.16763390.1766730.9650.98399.92510.145
2.83-3.0020.2143250.16160220.16363520.9720.98499.92130.141
3.002-3.2080.2222910.16956590.17159510.9680.98399.98320.152
3.208-3.4640.212430.16353060.16555520.9730.98599.9460.151
3.464-3.7930.2062370.16448810.16651180.9760.9851000.152
3.793-4.2390.1862030.13145110.13347140.980.9911000.124
4.239-4.890.1492210.1139180.11241390.9880.9941000.105
4.89-5.9780.1691490.12833990.1335480.9830.9911000.123
5.978-8.4060.1721460.1526550.15128010.9810.9871000.144
8.406-56.0950.223760.22416060.22416870.9380.95899.70360.238

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